The only classes, that are also available in KMS, whose unstackable Link Skills only have a max level of 2 are Cadena, Illium, Kinesis, Shade, and Xenon. I feel that adding level 3 to their Link Skills wouldn't cause too much power creep.
Cadena: Level 3 would imply 9% Damage per condition met, adding up to 18% Damage with both conditions. Although 18% Damage looks too OP for a Link Skill, there are 2 pieces of evidence that would push for a level 3. One, Demon Avenger's Link Skill has a level 3 that gives 15% Damage, only 3% less than Cadena's hypothetical level 3 link. And two, regular Damage has diminishing returns, meaning it's less effective the more regular Damage you have prior to activating Cadena's link.
Illium: Level 3 would imply 3% Damage per stack, adding up to 18% Damage at max stacks. See my argument with Cadena's link.
Kinesis: Level 3 would imply 6% Critical Damage. Before the V update, level 3 would have implied 12% Minimum Critical Damage, which would have been too OP, because most classes would only have a 3% Crit Damage difference, resulting in extremely consistent critical hits. With the Min Crit and Max Crit merge, the Crit Damage difference is always 30%, which made it strictly worse for most classes. Therefore, 6% Crit Damage wouldn't be very OP.
Shade: Level 3 would imply 15% Death Ignore Chance. 10% is the same rate as the most common success rate on Clean Slate Scrolls, and we all know how long and expensive it is to recover 1 upgrade slot. 15% is the same rate as the Weapon Spell Trace Scroll with the most amount of ATT, and it's barely easier than 10% CSS. Therefore, 15% Death Ignore Chance wouldn't be too OP.
Xenon: Level 3 would imply 15% All Stats. When Xenon was first released, GMS declared that his Link Skill at level 3 would be too OP. But one thing to keep in mind is his Link Skill has diminishing returns. Meaning the more All Stat percentage boost you have without his Link Skill, the smaller your overall All Stat increase will be when you activate his Link Skill. I feel that diminishing returns would make 15% All Stats not as OP as people would think.
As a bonus, Hayato and Kanna's Link Skills should also have a level 3, since I heard TMS was supposed to have level 3 added to them.
Hayato: Level 3 would imply 35 All Stat and 25 Weapon/Magic ATT. Diminishing returns says hi.
Kanna: Level 3 would imply 15% Damage. Literally the same as Demon Avenger's Link Skill.